If you’re new to QuickBooks, you may be wondering about what actually happens once a customer clicks that “Pay Now” button. Where does the money go? When will it reach your bank account? How will it show up in your books?
Essentially, what you’re hoping to answer is, “How does QuickBooks Payments work?” And when you’re searching for this information, we know you’re looking for a clear answer without technical confusion.
That’s what we’ll provide you with in this guide as we walk through setup, payment methods, processing, fees, deposits, and bookkeeping sync inside QuickBooks.
Here at Method CRM, we’ve been supporting QuickBooks-based businesses since 2010. Method is known for its real-time two-way QuickBooks sync, customization services, and end-to-end sales automation.
In this article, we’re going to uncover how Intuit QuickBooks Payments works and where Method fits around it so your accounting remains accurate while your workflows stay organized.
Table of Contents
- What is QuickBooks payments? 🤔
- Key benefits for small businesses ✅
- How to set up QuickBooks payments ⚙️
- Payment methods you can accept 💳
- How payments are processed 🧾
- Pricing & processing fees 💵
- How payments sync with QuickBooks bookkeeping 🔄
- QuickBooks payments with QuickBooks Desktop 🖥️
- Payment gateways beyond QuickBooks Payments 💰
- Common questions 🧐
- Conclusion 💬
- Frequently asked questions
What is QuickBooks payments? 🤔
QuickBooks Payments is the built-in payment processing service from Intuit. The platform allows businesses to accept online customer payments directly within a QuickBooks Online account or QuickBooks Desktop.
It connects invoices, sales receipts, and payment links to a merchant account. This way, customers can pay with a credit card, debit card, or ACH bank transfer. Once approved, payments post back into your bookkeeping automatically.
Unlike standalone gateways like Stripe or PayPal, QuickBooks Payments is meant to work natively within the QuickBooks ecosystem.
The accounting system and the payment processor are closely connected. In turn, you’re left with less manual data entry and cleaner records.
Key benefits for small businesses ✅
QuickBooks Payments appeals to accounting-first businesses that want payment activity tied directly to bookkeeping.
As mentioned above, integrated bookkeeping reduces manual entry. When a customer pays an invoice, QuickBooks marks it as paid and prepares a deposit record that matches your bank feed.
Multiple payment methods give customers flexibility. You can accept credit cards, debit cards, and ACH transfers.
Faster invoice payments improve cash flow visibility. Customers can click a payment link from the invoice itself. This cuts down on any payment friction while also shortening the payment cycle.
How to set up QuickBooks payments ⚙️
Next, let’s move on to some of the steps to follow, information you’ll need, and decisions you’ll have to make when setting up QuickBooks Payments.
Creating your QuickBooks payments account
Setup begins inside QuickBooks Online under “Account” and then “Account and Settings” in the Payments tab. Then, pick “Learn More” to sign up.
You’ll also need to add business details, owner info, and pick the account you want deposits to land in.
QuickBooks reviews your application as part of its merchant account approval process.
QuickBooks Desktop has a similar enrollment path, though features and pricing structures may differ depending on your plan.
Verifying your account & bank link-up
Intuit may request identity verification documents to confirm your business and principal officer details.
You connect your checking account for automated deposits. Some accounts require micro-deposit verification—this can take a few business days.
Once approved, you’re able to turn on online payments for customer invoices and start accepting funds!
Payment methods you can accept 💳
QuickBooks Payments supports major card networks, including Visa, Mastercard, Discover, and American Express. It also may support Apple Pay for eligible e-invoices.
You’ve also got point-of-sale options when it comes to how you accept payments:
- Online through emailed invoices with a Pay Now button
- Shareable payment links for online invoices
- In person (with a QuickBooks card reader or mobile app)
- ACH bank transfers
- Autopay for recurring invoices
How payments are processed 🧾
Card transactions follow three main stages in QuickBooks Payments:
- Authorization: The customer’s bank approves the charge and places a temporary hold on funds.
- Settlement: At the end of the business day, approved transactions are grouped into a batch and submitted for clearing.
- Funding: After settlement, money transfers to your linked bank account based on the deposit schedule.
If your transaction is processed before the daily cutoff of 3 PM PT, it will likely deposit the next business day. If it’s deposited later, payment processing times can be two days.
ACH transfers can follow a slightly different timeline. As Intuit explains, these can be delayed due to extra security measures.
Security is built into the payment processing process. QuickBooks Payments uses PCI-compliant infrastructure to help secure cardholder data during payment processing. Intuit manages the secure handling and transmission of payment information, while businesses remain responsible for maintaining compliant access controls and usage within their QuickBooks account.
Pricing & processing fees 💵
QuickBooks Payments uses a transparent pricing structure based on payment type.
Card payments through invoices typically carry a percentage-based processing fee of 2.99%. In-person swiped transactions have a different rate than manually keyed entries—2.5%.
ACH bank transfers usually cost less than credit card payments. With QuickBooks Payments, you’ll usually be charged a flat 1% fee.
Instant deposits are optional and come with an additional fee if you choose same-day funding.
There isn’t a separate monthly subscription required for standard QuickBooks Payments accounts, though QuickBooks Desktop may offer plan variations with different rate structures.
Processing fees are recorded in QuickBooks and can be mapped to an expense account so they appear clearly in financial reports. Tracking these monthly fees gives you helpful insights into true transaction costs over time.
How payments sync with QuickBooks bookkeeping 🔄
One of QuickBooks Payments’ biggest perks is automatic synchronization.
QuickBooks marks an invoice as “paid” once a customer completes their payment. Then, the platform also creates a corresponding deposit record that can match directly to your bank feed.
You’ll designate an expense account during setup, and this way, processing fees can be deducted and documented accordingly.
This built-in posting reduces reconciliation friction and can streamline accurate revenue reporting.
However, QuickBooks Payments focuses on collecting money and updating accounting records.
What it doesn’t do is:
- Manage approval workflows
- Handle job-level billing rules
- Perform multi-step follow-ups across teams
That is where Method steps up to fill in the gaps.
Method acts as the workflow layer around QuickBooks, before and after payment. Sales teams can move from quote to invoice with structured approval steps in place and operations teams can view payment statuses without needing access to accounting settings.
All data remains synced with QuickBooks in real time, so accounting stays the source of truth.
Customization in Method happens through collaboration with the Method team. You’re able to adapt screens, fields, and processes to match how you operate, rather than relying on rigid templates.
Transparency around that customization process helps set accurate expectations from the start.
QuickBooks payments with QuickBooks Desktop 🖥️
QuickBooks Desktop users can also accept payments, though the experience differs slightly from QuickBooks Online.
Desktop plans may include pay-as-you-go or monthly rate options. Swiped, invoiced, and keyed transactions can carry different processing percentages.
Auth-only transactions are available in some Desktop workflows. This way, you can authorize a card first and capture the charge later.
Deposit timing still follows daily batch processing rules, and instant deposit options may be available depending on the plan.
Payment gateways beyond QuickBooks Payments 💰
While QuickBooks Payments is built directly into QuickBooks, some businesses explore other gateways such as Stripe and PayPal, to manage processing fees, recurring billing, or custom checkout experiences.
These gateways may offer different pricing structures, subscription handling, or ecommerce flexibility depending on your business model.
How Method supports multiple payment options
Method does not replace your payment processor. Instead, it enhances your QuickBooks based payment workflows.
Method supports:
- QuickBooks Payments (QuickBooks Online)
- Stripe
- Authorize.Net
Braintree - PayPal
When payments are successfully recorded in QuickBooks, Method keeps invoices, payment status, and customer records synced across teams.
Common questions 🧐
Let’s review common QuickBooks Payments questions.
How long does it take for funds to hit your bank account?
This will depend on a few things, including the time your payment is processed (i.e., if it’s before or after the 3 PM PT cutoff). The chosen payment option matters too—ACH payments tend to take longer thanks to additional security checkpoints.
How do refunds and chargebacks work?
You can issue a refund from right within QuickBooks and return the funds to the original payment method.
Chargebacks require attention. If a customer disputes a transaction, Intuit notifies you with instructions for response and documentation. These are worth trying to avoid, as Intuit charges a $25 fee to cover the credit card processing costs for reversed payments.
What should I do if a payment fails?
If a payment fails, QuickBooks will flag the invoice so you’re aware of the problem. Next, you can follow up with the customer and request a new payment method.
Conclusion 💬
QuickBooks Payments makes it simple to accept credit cards and ACH transfers inside QuickBooks.
For some small businesses, that integration might be enough.
But the bottom line is, as companies grow, workflows around those payments often become more complex. Approval processes, job tracking, and cross-team visibility require structure beyond what accounting software alone provides.
Method provides this much-needed structure by supporting the business processes that surround QuickBooks (the accounting source of truth) and QuickBooks Payments (which collects the money).
If you want to see how Method connects your quotes, invoices, and payment status into one fully synced workflow, schedule a demo or start a free trial and evaluate how it fits your operation.
Frequently asked questions
When someone pays me through QuickBooks, where does the money go?
The money goes from the customer’s bank to your merchant services account during the authorization and settlement process. After that, deposits are transferred to your linked bank account based on the deposit schedule.
How do I start accepting payments?
Go to Account and Settings inside QuickBooks Online, open the Payments tab, and complete the application. After approval and bank verification, enable online payments on your invoices.
Can I accept payments with QuickBooks Desktop?
Yes. QuickBooks Desktop users can enroll in QuickBooks Payments and accept card and ACH transactions within their Desktop environment.
